Scoring an Approximate Matching
We need a way of scoring the quality of an approximate matching.
A scoring function is a mapping s from {A, C, G, T, -}2 to integers.
- The quantity s(x,y) is the score of a pair of symbols, x and y.
Example:
- s(x,y) = +2 if x=y and x in {A,C,G,T}
- s(x,y) = -1 otherwise